Preprocessing of Mouse AD Hippocampal DIA Data - C2

Metadata

Experiment

CrossTab: Sex


 
   Cell Contents
|-------------------------|
|                       N |
| Chi-square contribution |
|           N / Row Total |
|           N / Col Total |
|         N / Table Total |
|-------------------------|

 
Total Observations in Table:  153 

 
                         | Genotype (5=FAD, 0=WT) 
Sex (11=Female, 22=Male) |         0 |         5 |        na | Row Total | 
-------------------------|-----------|-----------|-----------|-----------|
                      11 |        31 |        30 |         0 |        61 | 
                         |     0.342 |     0.949 |     7.974 |           | 
                         |     0.508 |     0.492 |     0.000 |     0.399 | 
                         |     0.443 |     0.476 |     0.000 |           | 
                         |     0.203 |     0.196 |     0.000 |           | 
-------------------------|-----------|-----------|-----------|-----------|
                      22 |        39 |        33 |         0 |        72 | 
                         |     1.114 |     0.379 |     9.412 |           | 
                         |     0.542 |     0.458 |     0.000 |     0.471 | 
                         |     0.557 |     0.524 |     0.000 |           | 
                         |     0.255 |     0.216 |     0.000 |           | 
-------------------------|-----------|-----------|-----------|-----------|
                      na |         0 |         0 |        20 |        20 | 
                         |     9.150 |     8.235 |   115.614 |           | 
                         |     0.000 |     0.000 |     1.000 |     0.131 | 
                         |     0.000 |     0.000 |     1.000 |           | 
                         |     0.000 |     0.000 |     0.131 |           | 
-------------------------|-----------|-----------|-----------|-----------|
            Column Total |        70 |        63 |        20 |       153 | 
                         |     0.458 |     0.412 |     0.131 |           | 
-------------------------|-----------|-----------|-----------|-----------|

 

CrossTab: Age


 
   Cell Contents
|-------------------------|
|                       N |
| Chi-square contribution |
|           N / Row Total |
|           N / Col Total |
|         N / Table Total |
|-------------------------|

 
Total Observations in Table:  153 

 
                               | Genotype (5=FAD, 0=WT) 
Age Harvested (6=young,14=old) |         0 |         5 |        na | Row Total | 
-------------------------------|-----------|-----------|-----------|-----------|
                            14 |        34 |        29 |         0 |        63 | 
                               |     0.930 |     0.361 |     8.235 |           | 
                               |     0.540 |     0.460 |     0.000 |     0.412 | 
                               |     0.486 |     0.460 |     0.000 |           | 
                               |     0.222 |     0.190 |     0.000 |           | 
-------------------------------|-----------|-----------|-----------|-----------|
                             6 |        36 |        34 |         0 |        70 | 
                               |     0.493 |     0.930 |     9.150 |           | 
                               |     0.514 |     0.486 |     0.000 |     0.458 | 
                               |     0.514 |     0.540 |     0.000 |           | 
                               |     0.235 |     0.222 |     0.000 |           | 
-------------------------------|-----------|-----------|-----------|-----------|
                            na |         0 |         0 |        20 |        20 | 
                               |     9.150 |     8.235 |   115.614 |           | 
                               |     0.000 |     0.000 |     1.000 |     0.131 | 
                               |     0.000 |     0.000 |     1.000 |           | 
                               |     0.000 |     0.000 |     0.131 |           | 
-------------------------------|-----------|-----------|-----------|-----------|
                  Column Total |        70 |        63 |        20 |       153 | 
                               |     0.458 |     0.412 |     0.131 |           | 
-------------------------------|-----------|-----------|-----------|-----------|

 



Data Sparcity

No Filter

Filter



Log2 Transformation



Median Normalization



Peptide/Protein Group Inference

Protein groups are identified adopting the method used in MSDaPl [@Sharma2012] in which the parsimonious protein inference implemented is based on the IDPicker algorithm [@Ma2009]. The steps involved in the grouping of the indistinguishable protein groups are as follows:

  • Step 1: A bipartitie graph is created with edges between peptides and their matching proteins.


  • Step 2: Peptides that match the same set of proteins are merged into a single node in the graph. For example, peptides 3, 7, and 9 match protein A and no other protein.


  • Step 3: Proteins that match the same set of peptide are merged into a single node in the graph. These proteins comprise an indistinguishable protein group.


In this experiment, we report 7627 protein groups and 77113 non-redundant peptides inferred from 84325 peptides measured.



Batch Effect Adjustment

Peptide Group

Condition

No Adjustment


Batch Adjustment


Batch

No Adjustment


Batch Adjustment


Age

No Adjustment


Batch Adjustment


Genotype

No Adjustment


Batch Adjustment


Protein Group

Condition

No Adjustment


Batch Adjustment


Batch

No Adjustment


Batch Adjustment


Age

No Adjustment


Batch Adjustment


Genotype

No Adjustment


Batch Adjustment




Relative Standard Deviation

Peptide Group

HC2R2

MBRH2

Protein Group

HC2R2

MBRH2

Session Info

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] tidyr_1.1.0           readxl_1.3.1          plotly_4.9.2.1       
 [4] ggridges_0.5.2        dplyr_1.0.0           ggplot2_3.3.2        
 [7] scidata_0.0.0.9000    readr_1.3.1           rmdformats_1.0.3.9000
[10] knitr_1.29            RevoUtils_11.0.2      RevoUtilsMath_11.0.0 

loaded via a namespace (and not attached):
 [1] gtools_3.8.2       tidyselect_1.1.0   xfun_0.21          purrr_0.3.4       
 [5] colorspace_1.4-1   vctrs_0.3.1        generics_0.0.2     htmltools_0.5.1   
 [9] viridisLite_0.3.0  yaml_2.2.1         rlang_0.4.7        pillar_1.4.6      
[13] glue_1.4.1         withr_2.2.0        RColorBrewer_1.1-2 lifecycle_0.2.0   
[17] plyr_1.8.6         stringr_1.4.0      munsell_0.5.0      gtable_0.3.0      
[21] cellranger_1.1.0   htmlwidgets_1.5.1  evaluate_0.14      labeling_0.3      
[25] crosstalk_1.1.0.1  Rcpp_1.0.5         scales_1.1.1       DT_0.14           
[29] gdata_2.18.0       jsonlite_1.6.1     farver_2.0.3       hms_0.5.3         
[33] digest_0.6.25      stringi_1.4.6      gmodels_2.18.1     bookdown_0.20     
[37] grid_4.0.2         tools_4.0.2        magrittr_1.5       lazyeval_0.2.2    
[41] tibble_3.0.2       crayon_1.3.4       pkgconfig_2.0.3    ellipsis_0.3.1    
[45] MASS_7.3-51.6      data.table_1.12.8  rmarkdown_2.10     httr_1.4.1        
[49] R6_2.3.0           compiler_4.0.2